I have a site that has multiple networks as subdirectories, a la http://wp.school.edu/artSchool as one network and http://wp.school.edu/computerServices as another network, both of which are meant to have sub-sites.
After upgrading to 3.1 I've had a couple problems -
- The plugin I used WP Multi-Network isn't available anymore, I hope only due to the Super Admin menu being gone. So I can't edit networks at all
- The network admin link always redirects to http://wp.school.edu/wp-admin/network/index.php so I can't make network changes to any network other than the root network (http://wp.school.edu/)
This has the net effect of making those networks more or less useless. I may have misunderstood something critical - are multi networks technically a hack/unsupported thing/bad idea? I upgraded to 3.1 when I saw the "network" enhancements, assuming mistakenly that multi-networks would get a boost, but it's been… well, I already said. ;-)